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  <span class="target" id="module-MDAnalysis.coordinates.PDB"></span><div class="section" id="pdb-structure-files-in-mdanalysis-mdanalysis-coordinates-pdb">
<h1>5.7. PDB structure files in MDAnalysis &#8212; <a class="reference internal" href="#module-MDAnalysis.coordinates.PDB" title="MDAnalysis.coordinates.PDB"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.coordinates.PDB</span></tt></a><a class="headerlink" href="#pdb-structure-files-in-mdanalysis-mdanalysis-coordinates-pdb" title="Permalink to this headline">¶</a></h1>
<p>MDAnalysis reads coordinates from PDB files and additional optional
data such as B-factors. It is also possible to substitute a PDB file
instead of PSF file in order to define the list of atoms (but no
connectivity information will be  available in this case).</p>
<p>The <tt class="xref py py-mod docutils literal"><span class="pre">PDB</span></tt> module makes heavy use of Biopython&#8217;s <tt class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></tt>:</p>
<blockquote>
<div><p>Hamelryck, T., Manderick, B. (2003) PDB parser and structure class
implemented in Python. Bioinformatics, 19, 2308-2310.</p>
<p><a class="reference external" href="http://biopython.org">http://biopython.org</a></p>
</div></blockquote>
<p>but replaces the standard PDB file parser with one that uses the
<tt class="xref py py-class docutils literal"><span class="pre">MDAnalysis.coordinates.pdb.extensions.SloppyStructureBuilder</span></tt>
to cope with very large pdb files as commonly encountered in MD
simulations.</p>
<dl class="class">
<dt id="MDAnalysis.coordinates.PDB.PDBReader">
<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDB.</tt><tt class="descname">PDBReader</tt><big>(</big><em>pdbfilename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBReader" title="Permalink to this definition">¶</a></dt>
<dd><p>Read a pdb file into a BioPython pdb structure.</p>
<p>The coordinates are also supplied as one numpy array and wrapped
into a Timestep object; attributes are set so that the PDBReader
object superficially resembles the DCDReader object.</p>
<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PDBReader.Writer">
<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBReader.Writer" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a strict PDBWriter for <em>filename</em>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
<dt><em>filename</em></dt>
<dd><p class="first last">filename of the output PDB file</p>
</dd>
</dl>
</td>
</tr>
<tr class="field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="MDAnalysis.coordinates.PDB.PDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PDBWriter</span></tt></a></p>
</td>
</tr>
</tbody>
</table>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="MDAnalysis.coordinates.PDB.PDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PDBWriter</span></tt></a> &#8216;s <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBWriter.write" title="MDAnalysis.coordinates.PDB.PDBWriter.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a> method
always requires a <tt class="xref py py-class docutils literal"><span class="pre">Timestep</span></tt> as an argument (it is
not optional anymore when the Writer is obtained through
this method of <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PDBReader" title="MDAnalysis.coordinates.PDB.PDBReader"><tt class="xref py py-class docutils literal"><span class="pre">PDBReader</span></tt></a>.)</p>
</div>
</dd></dl>

<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PDBReader.get_bfactors">
<tt class="descname">get_bfactors</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBReader.get_bfactors" title="Permalink to this definition">¶</a></dt>
<dd><p>Return an array of bfactors (tempFactor) in atom order.</p>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="MDAnalysis.coordinates.PDB.PDBWriter">
<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDB.</tt><tt class="descname">PDBWriter</tt><big>(</big><em>pdbfilename</em>, <em>universe=None</em>, <em>multi=False</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBWriter" title="Permalink to this definition">¶</a></dt>
<dd><p>Write out the current time step as a pdb file.</p>
<p>This is not cleanly implemented at the moment. One must supply a
universe, even though this is nominally an optional argument. The
class behaves slightly differently depending on if the structure
was loaded from a PDB (then the full-fledged <tt class="xref py py-mod docutils literal"><span class="pre">Bio.PDB</span></tt> writer is
used) or if this is really only an atom selection (then a less
sophistiocated writer is employed).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The standard PDBWriter can only write the <em>whole system</em>.  In
order to write a selection, use the <a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a>,
which happens automatically when the
<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.write" title="MDAnalysis.core.AtomGroup.AtomGroup.write"><tt class="xref py py-meth docutils literal"><span class="pre">write()</span></tt></a> method of a
<a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a> instance is used.</p>
</div>
<p>pdbwriter = PDBWriter(&lt;pdbfilename&gt;,universe=universe,**kwargs)
:Arguments:
pdbfilename     filename; if multi=True, embed a %%d formatstring</p>
<blockquote>
<div>so that write_next_timestep() can insert the frame number</div></blockquote>
<p>universe        supply a universe [really REQUIRED; optional only for compatibility]
multi           False: write a single structure to a single pdb</p>
<blockquote>
<div>True: write all frames to multiple pdb files</div></blockquote>
<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PDBWriter.write">
<tt class="descname">write</tt><big>(</big><em>ts=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PDBWriter.write" title="Permalink to this definition">¶</a></dt>
<dd><p>Write timestep as a pdb file.</p>
<p>If ts=None then we try to get the current one from the universe.</p>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="MDAnalysis.coordinates.PDB.PrimitivePDBReader">
<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDB.</tt><tt class="descname">PrimitivePDBReader</tt><big>(</big><em>filename</em>, <em>convert_units=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader" title="Permalink to this definition">¶</a></dt>
<dd><p>PDBReader that reads a PDB-formatted file, no frills.</p>
<dl class="docutils">
<dt>Records read:</dt>
<dd><ul class="first last simple">
<li>CRYST1 for unitcell A,B,C, alpha,beta,gamm</li>
<li>ATOM. HETATM for x,y,z</li>
</ul>
</dd>
</dl>
<p><a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html">http://www.wwpdb.org/documentation/format32/sect9.html</a></p>
<table border="1" class="docutils">
<colgroup>
<col width="16%" />
<col width="15%" />
<col width="14%" />
<col width="56%" />
</colgroup>
<thead valign="bottom">
<tr><th class="head">COLUMNS</th>
<th class="head">DATA  TYPE</th>
<th class="head">FIELD</th>
<th class="head">DEFINITION</th>
</tr>
</thead>
<tbody valign="top">
<tr><td>1 -  6</td>
<td>Record name</td>
<td>&#8220;CRYST1&#8221;</td>
<td>&nbsp;</td>
</tr>
<tr><td>7 - 15</td>
<td>Real(9.3)</td>
<td>a</td>
<td>a (Angstroms).</td>
</tr>
<tr><td>16 - 24</td>
<td>Real(9.3)</td>
<td>b</td>
<td>b (Angstroms).</td>
</tr>
<tr><td>25 - 33</td>
<td>Real(9.3)</td>
<td>c</td>
<td>c (Angstroms).</td>
</tr>
<tr><td>34 - 40</td>
<td>Real(7.2)</td>
<td>alpha</td>
<td>alpha (degrees).</td>
</tr>
<tr><td>41 - 47</td>
<td>Real(7.2)</td>
<td>beta</td>
<td>beta (degrees).</td>
</tr>
<tr><td>48 - 54</td>
<td>Real(7.2)</td>
<td>gamma</td>
<td>gamma (degrees).</td>
</tr>
<tr><td>1 -  6</td>
<td>Record name</td>
<td>&#8220;ATOM  &#8220;</td>
<td>&nbsp;</td>
</tr>
<tr><td>7 - 11</td>
<td>Integer</td>
<td>serial</td>
<td>Atom  serial number.</td>
</tr>
<tr><td>13 - 16</td>
<td>Atom</td>
<td>name</td>
<td>Atom name.</td>
</tr>
<tr><td>17</td>
<td>Character</td>
<td>altLoc</td>
<td>Alternate location indicator. IGNORED</td>
</tr>
<tr><td>18 - 21</td>
<td>Residue name</td>
<td>resName</td>
<td>Residue name.</td>
</tr>
<tr><td>22</td>
<td>Character</td>
<td>chainID</td>
<td>Chain identifier.</td>
</tr>
<tr><td>23 - 26</td>
<td>Integer</td>
<td>resSeq</td>
<td>Residue sequence number.</td>
</tr>
<tr><td>27</td>
<td>AChar</td>
<td>iCode</td>
<td>Code for insertion of residues. IGNORED</td>
</tr>
<tr><td>31 - 38</td>
<td>Real(8.3)</td>
<td>x</td>
<td>Orthogonal coordinates for X in Angstroms.</td>
</tr>
<tr><td>39 - 46</td>
<td>Real(8.3)</td>
<td>y</td>
<td>Orthogonal coordinates for Y in Angstroms.</td>
</tr>
<tr><td>47 - 54</td>
<td>Real(8.3)</td>
<td>z</td>
<td>Orthogonal coordinates for Z in Angstroms.</td>
</tr>
<tr><td>55 - 60</td>
<td>Real(6.2)</td>
<td>occupancy</td>
<td>Occupancy.</td>
</tr>
<tr><td>61 - 66</td>
<td>Real(6.2)</td>
<td>tempFactor</td>
<td>Temperature  factor.</td>
</tr>
<tr><td>67 - 76</td>
<td>String</td>
<td>segID</td>
<td>(unofficial CHARMM extension ?)</td>
</tr>
<tr><td>77 - 78</td>
<td>LString(2)</td>
<td>element</td>
<td>Element symbol, right-justified. IGNORED</td>
</tr>
<tr><td>79 - 80</td>
<td>LString(2)</td>
<td>charge</td>
<td>Charge  on the atom. IGNORED</td>
</tr>
</tbody>
</table>
<p>Read coordinates from <em>filename</em>.</p>
<p><em>filename</em> can be a gzipped or bzip2ed compressed PDB file.</p>
<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PrimitivePDBReader.Writer">
<tt class="descname">Writer</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader.Writer" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a permissive (simple) PDBWriter for <em>filename</em>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first docutils">
<dt><em>filename</em></dt>
<dd><p class="first last">filename of the output PDB file</p>
</dd>
</dl>
</td>
</tr>
<tr class="field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last"><a class="reference internal" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="MDAnalysis.coordinates.PDB.PrimitivePDBWriter"><tt class="xref py py-class docutils literal"><span class="pre">PrimitivePDBWriter</span></tt></a></p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PrimitivePDBReader.get_bfactors">
<tt class="descname">get_bfactors</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader.get_bfactors" title="Permalink to this definition">¶</a></dt>
<dd><p>Return an array of bfactors (tempFactor) in atom order.</p>
</dd></dl>

<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PrimitivePDBReader.get_occupancy">
<tt class="descname">get_occupancy</tt><big>(</big><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBReader.get_occupancy" title="Permalink to this definition">¶</a></dt>
<dd><p>Return an array of occupancies in atom order.</p>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter">
<em class="property">class </em><tt class="descclassname">MDAnalysis.coordinates.PDB.</tt><tt class="descname">PrimitivePDBWriter</tt><big>(</big><em>filename</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter" title="Permalink to this definition">¶</a></dt>
<dd><p>PDB writer that implements a subset of the PDB 3.2 standard.
<a class="reference external" href="http://www.wwpdb.org/documentation/format32/v3.2.html">http://www.wwpdb.org/documentation/format32/v3.2.html</a></p>
<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ATOM">
<tt class="descname">ATOM</tt><big>(</big><em>serial=None</em>, <em>name=None</em>, <em>altLoc=None</em>, <em>resName=None</em>, <em>chainID=None</em>, <em>resSeq=None</em>, <em>iCode=None</em>, <em>x=None</em>, <em>y=None</em>, <em>z=None</em>, <em>occupancy=1.0</em>, <em>tempFactor=0.0</em>, <em>segID=None</em>, <em>element=None</em>, <em>charge=0</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ATOM" title="Permalink to this definition">¶</a></dt>
<dd><p>Write ATOM record.
<a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect9.html">http://www.wwpdb.org/documentation/format32/sect9.html</a>
Only some keword args are optional (altLoc, iCode, chainID), for some defaults are set.</p>
<p>All inputs are cut to the maximum allowed length. For integer
numbers the highest-value digits are chopped (so that the
serial and reSeq wrap); for strings the trailing characters
are chopped.</p>
<p>Note: Floats are not checked and can potentially screw up the format.</p>
</dd></dl>

<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.CRYST1">
<tt class="descname">CRYST1</tt><big>(</big><em>dimensions</em>, <em>spacegroup='P 1'</em>, <em>zvalue=1</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.CRYST1" title="Permalink to this definition">¶</a></dt>
<dd><p>Write CRYST1 record.
<a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect8.html">http://www.wwpdb.org/documentation/format32/sect8.html</a></p>
</dd></dl>

<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.REMARK">
<tt class="descname">REMARK</tt><big>(</big><em>*remark</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.REMARK" title="Permalink to this definition">¶</a></dt>
<dd><p>Write generic REMARK record (without number).
<a class="reference external" href="http://www.wwpdb.org/documentation/format32/remarks1.html">http://www.wwpdb.org/documentation/format32/remarks1.html</a>
<a class="reference external" href="http://www.wwpdb.org/documentation/format32/remarks2.html">http://www.wwpdb.org/documentation/format32/remarks2.html</a></p>
</dd></dl>

<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.TITLE">
<tt class="descname">TITLE</tt><big>(</big><em>*title</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.TITLE" title="Permalink to this definition">¶</a></dt>
<dd><p>Write TITLE record.
<a class="reference external" href="http://www.wwpdb.org/documentation/format32/sect2.html">http://www.wwpdb.org/documentation/format32/sect2.html</a></p>
</dd></dl>

<dl class="method">
<dt id="MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write">
<tt class="descname">write</tt><big>(</big><em>selection</em>, <em>frame=None</em><big>)</big><a class="headerlink" href="#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write" title="Permalink to this definition">¶</a></dt>
<dd><p>Write selection at current trajectory frame to file.</p>
<p>write(selection,frame=FRAME)</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field"><th class="field-name">Arguments :</th><td class="field-body"><dl class="first last docutils">
<dt><em>selection</em></dt>
<dd><p class="first last">a <a class="reference internal" href="../core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup" title="MDAnalysis.core.AtomGroup.AtomGroup"><tt class="xref py py-class docutils literal"><span class="pre">AtomGroup</span></tt></a></p>
</dd>
<dt><em>frame</em></dt>
<dd><p class="first last">optionally move to frame <em>FRAME</em></p>
</dd>
</dl>
</td>
</tr>
</tbody>
</table>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The first letter of the <tt class="xref py py-attr docutils literal"><span class="pre">segid</span></tt>
is used as the PDB chainID.</p>
</div>
</dd></dl>

</dd></dl>

</div>


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